Variant report

Variant	rs6453253
Chromosome Location	chr5:76134777-76134778
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:76134716-76135138	HCT-116	colon:	n/a	n/a
2	FOS	chr5:76134413-76135058	Hela-S3	cervix:	n/a	chr5:76134890-76134900 chr5:76134891-76134899 chr5:76134889-76134901 chr5:76134890-76134900 chr5:76134890-76134900
3	FOSL2	chr5:76134744-76134980	A549	lung:	n/a	chr5:76134890-76134900 chr5:76134891-76134899 chr5:76134889-76134901 chr5:76134890-76134900 chr5:76134890-76134900
4	SP1	chr5:76134039-76135403	HCT-116	colon:	n/a	n/a
5	POLR2A	chr5:76134021-76135436	PANC-1	pancreas:	n/a	n/a
6	TCF12	chr5:76134286-76135200	SK-N-SH	brain:	n/a	n/a
7	SP1	chr5:76134020-76135446	HCT-116	colon:	n/a	n/a
8	JUND	chr5:76134727-76135319	A549	lung:	n/a	chr5:76134890-76134900 chr5:76134891-76134899 chr5:76134889-76134901 chr5:76134890-76134900 chr5:76134890-76134900
9	JUND	chr5:76134100-76135393	HCT-116	colon:	n/a	chr5:76134890-76134900 chr5:76134891-76134899 chr5:76134889-76134901 chr5:76134890-76134900 chr5:76134890-76134900
10	TEAD4	chr5:76134546-76135178	HCT-116	colon:	n/a	n/a
11	TCF7L2	chr5:76134172-76135102	HCT-116	colon:	n/a	n/a
12	JUN	chr5:76134736-76134923	H1-hESC	embryonic stem cell:	n/a	chr5:76134890-76134900 chr5:76134891-76134899 chr5:76134889-76134901 chr5:76134890-76134900 chr5:76134890-76134900
13	GATA3	chr5:76134272-76135147	SK-N-SH	brain:	n/a	chr5:76134889-76134898 chr5:76134892-76134901 chr5:76134700-76134709
14	FOSL2	chr5:76134483-76135163	A549	lung:	n/a	chr5:76134890-76134900 chr5:76134891-76134899 chr5:76134889-76134901 chr5:76134890-76134900 chr5:76134890-76134900
15	E2F4	chr5:76134753-76135031	MCF10A-Er-Src	breast:	n/a	n/a
16	EP300	chr5:76134186-76134926	ECC-1	luminal epithelium:	n/a	n/a
17	SETDB1	chr5:76134335-76135024	U2OS	brain:	n/a	n/a
18	POLR2A	chr5:76131046-76138228	A549	lung:	n/a	n/a
19	GATA3	chr5:76134173-76135207	SK-N-SH	brain:	n/a	chr5:76134889-76134898 chr5:76134892-76134901 chr5:76134700-76134709
20	PBX3	chr5:76134203-76135218	SK-N-SH	brain:	n/a	n/a
21	KAP1	chr5:76134259-76135054	U2OS	brain:	n/a	n/a
22	TEAD4	chr5:76134320-76135157	ECC-1	luminal epithelium:	n/a	n/a
23	POLR2A	chr5:76134083-76135438	PFSK-1	brain:	n/a	n/a
24	FOSL1	chr5:76134070-76135382	HCT-116	colon:	n/a	chr5:76134890-76134900 chr5:76134891-76134899 chr5:76134889-76134901 chr5:76134890-76134900 chr5:76134890-76134900
25	POLR2A	chr5:76134100-76135356	PANC-1	pancreas:	n/a	n/a
26	YY1	chr5:76134761-76135040	HCT-116	colon:	n/a	n/a
27	FOSL1	chr5:76134223-76135340	HCT-116	colon:	n/a	chr5:76134890-76134900 chr5:76134891-76134899 chr5:76134889-76134901 chr5:76134890-76134900 chr5:76134890-76134900
28	FOXM1	chr5:76134352-76134945	ECC-1	luminal epithelium:	n/a	n/a
29	POLR2A	chr5:76134017-76135348	HCT-116	colon:	n/a	n/a
30	NR3C1	chr5:76134528-76135028	A549	lung:	n/a	chr5:76134891-76134900 chr5:76134670-76134684
31	POLR2A	chr5:76134590-76135384	PFSK-1	brain:	n/a	n/a
32	TEAD4	chr5:76134573-76135250	HCT-116	colon:	n/a	n/a
33	MAX	chr5:76134236-76135054	Hela-S3	cervix:	n/a	n/a
34	JUND	chr5:76134037-76135460	HCT-116	colon:	n/a	chr5:76134890-76134900 chr5:76134891-76134899 chr5:76134889-76134901 chr5:76134890-76134900 chr5:76134890-76134900
35	JUND	chr5:76134431-76135059	Hela-S3	cervix:	n/a	chr5:76134890-76134900 chr5:76134891-76134899 chr5:76134889-76134901 chr5:76134890-76134900 chr5:76134890-76134900
36	JUND	chr5:76134592-76135063	A549	lung:	n/a	chr5:76134890-76134900 chr5:76134891-76134899 chr5:76134889-76134901 chr5:76134890-76134900 chr5:76134890-76134900
37	TCF7L2	chr5:76134350-76134824	PANC-1	pancreas:	n/a	n/a
38	CEBPB	chr5:76134470-76135001	Hela-S3	cervix:	n/a	n/a

Variant related genes	Relation type
RN7SL208P	TF binding region

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10053003	0.89[ASN][1000 genomes]
rs10058498	0.83[EUR][1000 genomes]
rs1030484	0.91[ASN][1000 genomes]
rs12186639	0.93[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs13157422	0.92[ASN][1000 genomes]
rs13166089	0.82[ASN][1000 genomes]
rs13177258	0.92[ASN][1000 genomes]
rs13179180	0.83[ASN][1000 genomes]
rs13179405	0.85[ASN][1000 genomes]
rs1529505	0.84[CEU][hapmap]
rs1963861	0.89[ASN][1000 genomes]
rs2243003	0.88[CEU][hapmap]
rs2243010	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs2243022	0.88[CEU][hapmap]
rs2243029	0.84[EUR][1000 genomes]
rs2243051	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs2243053	0.85[EUR][1000 genomes]
rs2243057	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs2243059	0.85[EUR][1000 genomes]
rs2434656	0.83[ASN][1000 genomes]
rs3135471	0.83[ASN][1000 genomes]
rs34469953	0.90[ASN][1000 genomes]
rs3925483	0.84[ASN][1000 genomes]
rs4591731	0.88[CEU][hapmap]
rs4704366	0.83[ASN][1000 genomes]
rs55925929	0.86[ASN][1000 genomes]
rs56238109	0.87[ASN][1000 genomes]
rs62365101	0.90[ASN][1000 genomes]
rs62365104	0.92[ASN][1000 genomes]
rs62365105	0.92[ASN][1000 genomes]
rs6453251	0.88[CEU][hapmap]
rs66946336	0.85[EUR][1000 genomes]
rs6880329	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs6897362	0.88[CEU][hapmap]
rs7703930	0.88[CEU][hapmap]
rs7709688	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs7712660	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1019669	chr5:75836365-76477788	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	esv2763908	chr5:76083394-76134777	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv882210	chr5:76086597-76140337	Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv1025151	chr5:76086795-76134777	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	esv3393424	chr5:76122720-76287744	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	esv994503	chr5:76129230-76144182	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv2762526	chr5:76134777-76153934	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6453253	F2RL1	cis	multi-tissue	Pritchard
rs6453253	F2RL1	cis	Whole Blood	GTEx
rs6453253	F2R	cis	Muscle Skeletal	GTEx

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:76117400-76135200	Weak transcription	Colonic Mucosa	Colon
2	chr5:76129200-76134800	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr5:76129400-76134800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr5:76129800-76135800	Weak transcription	Pancreas	Pancrea
5	chr5:76130200-76134800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:76130200-76135800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr5:76130200-76137200	Weak transcription	Esophagus	oesophagus
8	chr5:76130400-76135600	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr5:76130400-76140400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr5:76130800-76134800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr5:76132200-76135400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr5:76132200-76145800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr5:76132800-76136800	Enhancers	Fetal Intestine Large	intestine
14	chr5:76133000-76134800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr5:76133000-76135000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr5:76133000-76135000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr5:76133600-76136800	Enhancers	Fetal Intestine Small	intestine
18	chr5:76133800-76135000	Enhancers	NHEK	skin
19	chr5:76133800-76135200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr5:76133800-76135200	Enhancers	HUVEC	blood vessel
21	chr5:76134000-76135200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:76134000-76135200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr5:76134000-76136000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr5:76134000-76136000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr5:76134200-76134800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr5:76134200-76135000	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr5:76134200-76135000	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr5:76134200-76135000	Enhancers	iPS-20b Cell Line	embryonic stem cell
29	chr5:76134200-76135000	Enhancers	Fetal Kidney	kidney
30	chr5:76134200-76135000	Enhancers	HMEC	breast
31	chr5:76134200-76135000	Flanking Active TSS	NH-A	brain
32	chr5:76134200-76135200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr5:76134200-76135200	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr5:76134200-76135200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr5:76134200-76135200	Enhancers	Muscle Satellite Cultured Cells	--
36	chr5:76134200-76135200	Enhancers	Stomach Mucosa	stomach
37	chr5:76134200-76135400	Enhancers	NHDF-Ad	bronchial
38	chr5:76134200-76135400	Enhancers	Osteobl	bone
39	chr5:76134200-76135800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr5:76134200-76136000	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr5:76134200-76136000	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr5:76134200-76136200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr5:76134200-76136800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr5:76134400-76134800	Weak transcription	Gastric	stomach
45	chr5:76134400-76134800	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr5:76134400-76134800	Enhancers	A549	lung
47	chr5:76134400-76135000	Enhancers	Primary hematopoietic stem cells	blood
48	chr5:76134400-76135200	Flanking Active TSS	Hela-S3	cervix
49	chr5:76134400-76135200	Enhancers	NHLF	lung
50	chr5:76134400-76135400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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